Contacts of the helix formed by residues 79 - 89 (chain F) in PDB entry 1M06
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with GLY 79 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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75F ARG* 2.9 26.3 + - - +
76F HIS 4.5 1.5 - - - -
77F VAL 3.2 4.0 + - - -
78F TYR* 1.3 74.9 - - - +
80F ASP* 1.3 60.2 + - - -
82F TRP* 2.8 26.9 + - - +
83F ILE* 3.4 3.0 + - - -
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Residues in contact with ASP 80 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78F TYR 3.6 0.2 + - - -
79F GLY* 1.3 70.3 - - - -
81F GLN* 1.3 63.1 + - - +
83F ILE* 2.9 23.6 + - - +
84F GLN* 2.9 42.4 + - - +
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Residues in contact with GLN 81 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78F TYR* 3.0 22.9 + - + +
80F ASP* 1.3 78.9 - - - +
82F TRP* 1.3 53.8 + - - +
84F GLN* 3.7 7.8 + - - +
85F PHE* 3.1 24.3 + - - +
93F GLN 5.7 2.1 - - - +
94F PRO 5.0 1.6 - - - +
95F LEU* 4.3 11.4 - - + +
96F PRO* 3.2 38.3 - - - +
122F LYS* 5.6 5.9 - - - +
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Residues in contact with TRP 82 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74F HIS* 3.8 34.5 - + + -
75F ARG* 3.7 33.9 - - + +
78F TYR* 3.5 19.3 + + + +
79F GLY 2.8 11.6 + - - +
81F GLN* 1.3 76.7 - - - +
83F ILE* 1.3 73.4 + - + +
85F PHE* 2.8 38.6 + + - +
86F MET* 2.9 50.9 + - + +
95F LEU* 3.8 25.1 - - + -
280F GLU* 5.1 8.2 + - - +
281F HIS* 3.6 31.1 + + + +
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Residues in contact with ILE 83 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75F ARG* 4.0 30.5 - - + -
79F GLY 3.4 1.7 + - - +
80F ASP* 2.9 26.1 + - - +
82F TRP* 1.3 85.0 - - + +
84F GLN* 1.3 64.8 + - - +
86F MET* 3.3 4.7 + - - +
87F ARG* 2.8 54.8 + - + +
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Residues in contact with GLN 84 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80F ASP* 2.9 30.5 + - - +
81F GLN* 3.8 10.3 - - - +
83F ILE* 1.3 81.6 - - - +
85F PHE* 1.3 67.8 + - - +
87F ARG* 2.8 33.3 + - - +
88F ASP* 2.6 49.0 + - - +
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Residues in contact with PHE 85 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81F GLN 3.1 12.4 + - - +
82F TRP* 2.8 45.5 + + - +
84F GLN* 1.3 81.0 - - - +
86F MET* 1.3 72.5 + - - +
89F GLY* 3.0 18.2 + - - +
92F ALA* 3.4 33.4 - - + +
93F GLN 4.0 7.6 - - - +
94F PRO* 4.5 4.9 - - + -
95F LEU* 3.6 38.4 - - + -
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Residues in contact with MET 86 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82F TRP* 2.9 58.4 + - + +
83F ILE* 3.8 7.2 - - - +
85F PHE* 1.3 83.8 - - - +
87F ARG* 1.3 65.8 + - + +
89F GLY* 3.4 10.5 + - - +
281F HIS* 3.7 29.6 - - + +
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Residues in contact with ARG 87 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83F ILE* 2.8 43.3 + - + +
84F GLN* 2.8 41.2 + - - +
86F MET* 1.3 70.8 - - + +
88F ASP* 1.3 63.2 + - - +
89F GLY* 2.9 10.7 + - - -
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Residues in contact with ASP 88 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84F GLN* 2.6 50.3 + - - +
87F ARG* 1.3 74.1 + - - +
89F GLY* 1.3 63.6 + - - +
90F VAL* 3.2 1.6 + - - +
91F ASN* 3.0 26.9 + - + +
92F ALA* 3.8 22.2 - - - +
93F GLN 5.5 0.5 + - - -
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Residues in contact with GLY 89 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85F PHE* 3.0 11.4 + - - +
86F MET* 3.8 8.7 - - - -
87F ARG 2.9 7.1 - - - -
88F ASP* 1.3 77.4 - - - +
90F VAL* 1.3 53.5 + - - -
91F ASN 2.7 10.9 + - - -
92F ALA* 2.9 21.0 + - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il